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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaatctctagaatgagtttcctttcttaactaagataaatttatttaggtgttttgttctcacattcttttgtttctgtttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG

Basic information

species Zea mays
transcript GRMZM2G140328_T02
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 30
lower sequence: LOC_Os04g51610.1 (Oryza sativa), 3'ss of exon 31
----------------------------gtagaatctctagaatgagtttc-----ctttcttaactaagataaatttatttaggtgttttgttctcacattcttttgtttctgtttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG
|| || ||| | | | || | | | || | |||| || ||| | | || || | || |||||| || | |||||||||| ||||||||||||||||||||| | || || || || | ||||||||||||||||| || |||||||| || || || |
gtagaaaacccaccgtaataattcctccttactatatctgttactgggccctatagctgtttatatggagctgaattgatctagatctgttattggc-------ttcacatctgttaatgtgcagGCGCTTATTGTTGAGTTCCTTGGCAAGTTTACATCGACAACCAGACTCACCTGGCAGTTGTGGTTGGTGTCAATAGGTCTCGCCTTTTTTAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 30
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 31
----------------------------gtagaatctctagaatgagtttc-----ctttcttaactaagataaatttatttaggtgttttgttctcacattcttttgtttctgtttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG--------
|| || ||| | | | || | | | || | |||| || ||| | | || || | || |||||| || | |||||||||| ||||||||||||||||||||| | || || || || | ||||||||||||||||| || |||||||| || || || |
gtagaaaacccaccgtaataattcctccttactatatctgttactgggccctatagctgtttatatggagctgaattgatctagatctgttattggc-------ttcacatctgttaatgtgcagGCGCTTATTGTTGAGTTCCTTGGCAAGTTTACATCGACAACCAGACTCACCTGGCAGTTGTGGTTGGTGTCAATAGGTCTCGCCTTTTTTAGGTAAGCTC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|16925064|gb|BM078132.1|BM078132
EST:     CAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAG                         GCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGT
genomic: CAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAGgtagaatctc ... ttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGT




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 80

CGAATTCAATTCGCGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAGgtagaatctc ... ttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 12

CGAATTCAATTCGCGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAGgtagaatctc ... ttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 12

CGAATTCAATTCGCGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAGgtagaatctc ... ttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

CGAATTCAATTCGCGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTGTACTCCAGgtagaatctc ... ttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatttatttaggtgttttgttctcacattcttttgtttctgtttatatttagGCGCTTATCGTTGAGTTCCTTGGCAAGTTTGCCTCAACGGTAAGGCTAAGTTGGCAGTTGTGGTTGGTATCGATAGGTCTTGCTTTCTTCGG
                      ttctcac  putative branch site (score: 54)
 ttcttttgtttctgtt  CT-rich tract
 ttttgtttctgtttat  TA-rich tract